HEADER MEMBRANE PROTEIN 18-DEC-20 7BC7
TITLE CRYO-EM STRUCTURE OF THE PROTON COUPLED FOLATE TRANSPORTER AT PH 6.0
TITLE 2 BOUND TO PEMETREXED
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTON-COUPLED FOLATE TRANSPORTER;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: NANOBODY;
COMPND 7 CHAIN: B
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
SOURCE 3 ORGANISM_COMMON: CHICKEN;
SOURCE 4 ORGANISM_TAXID: 9031;
SOURCE 5 GENE: PCFT;
SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932;
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA;
SOURCE 10 ORGANISM_TAXID: 9844
KEYWDS TRANSPORTER FOLATE PROTON SYMPORTER, MEMBRANE PROTEIN
EXPDTA ELECTRON MICROSCOPY
AUTHOR J.L.PARKER,J.C.DEME,S.M.LEA,S.NEWSTEAD
REVDAT 6 23-OCT-24 7BC7 1 REMARK
REVDAT 5 11-AUG-21 7BC7 1 JRNL
REVDAT 4 14-JUL-21 7BC7 1 JRNL
REVDAT 3 07-JUL-21 7BC7 1 JRNL
REVDAT 2 09-JUN-21 7BC7 1 JRNL
REVDAT 1 12-MAY-21 7BC7 0
JRNL AUTH J.L.PARKER,J.C.DEME,G.KUTEYI,Z.WU,J.HUO,I.D.GOLDMAN,
JRNL AUTH 2 R.J.OWENS,P.C.BIGGIN,S.M.LEA,S.NEWSTEAD
JRNL TITL STRUCTURAL BASIS OF ANTIFOLATE RECOGNITION AND TRANSPORT BY
JRNL TITL 2 PCFT.
JRNL REF NATURE V. 595 130 2021
JRNL REFN ESSN 1476-4687
JRNL PMID 34040256
JRNL DOI 10.1038/S41586-021-03579-Z
REMARK 2
REMARK 2 RESOLUTION. 3.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 SOFTWARE PACKAGES : NULL
REMARK 3 RECONSTRUCTION SCHEMA : NULL
REMARK 3
REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT
REMARK 3 PDB ENTRY : NULL
REMARK 3 REFINEMENT SPACE : NULL
REMARK 3 REFINEMENT PROTOCOL : NULL
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL
REMARK 3
REMARK 3 FITTING PROCEDURE : NULL
REMARK 3
REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS
REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL
REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL
REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.300
REMARK 3 NUMBER OF PARTICLES : 341318
REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE
REMARK 3 CORRECTION
REMARK 3
REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL
REMARK 3
REMARK 3 OTHER DETAILS: NULL
REMARK 4
REMARK 4 7BC7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-20.
REMARK 100 THE DEPOSITION ID IS D_1292113113.
REMARK 245
REMARK 245 EXPERIMENTAL DETAILS
REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE
REMARK 245 SPECIMEN TYPE : NULL
REMARK 245
REMARK 245 ELECTRON MICROSCOPE SAMPLE
REMARK 245 SAMPLE TYPE : PARTICLE
REMARK 245 PARTICLE TYPE : POINT
REMARK 245 NAME OF SAMPLE : COMPLEX OF THE PROTON COUPLED
REMARK 245 FOLATE TRANSPORTER AT PH 6.0
REMARK 245 BOUND TO PEMETREXED; PROTON-
REMARK 245 COUPLED FOLATE TRANSPORTER;
REMARK 245 NANOBODY
REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL
REMARK 245 SAMPLE SUPPORT DETAILS : NULL
REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL
REMARK 245 SAMPLE BUFFER : NULL
REMARK 245 PH : 6.00
REMARK 245 SAMPLE DETAILS : NULL
REMARK 245
REMARK 245 DATA ACQUISITION
REMARK 245 DATE OF EXPERIMENT : NULL
REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL
REMARK 245 TEMPERATURE (KELVIN) : NULL
REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS
REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X
REMARK 245 4K)
REMARK 245 MINIMUM DEFOCUS (NM) : NULL
REMARK 245 MAXIMUM DEFOCUS (NM) : NULL
REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL
REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL
REMARK 245 NOMINAL CS : NULL
REMARK 245 IMAGING MODE : BRIGHT FIELD
REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5850.00
REMARK 245 ILLUMINATION MODE : FLOOD BEAM
REMARK 245 NOMINAL MAGNIFICATION : NULL
REMARK 245 CALIBRATED MAGNIFICATION : NULL
REMARK 245 SOURCE : FIELD EMISSION GUN
REMARK 245 ACCELERATION VOLTAGE (KV) : 300
REMARK 245 IMAGING DETAILS : NULL
REMARK 247
REMARK 247 ELECTRON MICROSCOPY
REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON
REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE
REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES
REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION
REMARK 247 OF THE STRUCTURE FACTORS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3090 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22480 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 ALA A 2
REMARK 465 ALA A 3
REMARK 465 PRO A 4
REMARK 465 SER A 5
REMARK 465 ASP A 6
REMARK 465 PRO A 7
REMARK 465 PRO A 8
REMARK 465 THR A 9
REMARK 465 ALA A 10
REMARK 465 ALA A 11
REMARK 465 THR A 12
REMARK 465 PRO A 13
REMARK 465 PRO A 14
REMARK 465 ALA A 15
REMARK 465 PRO A 16
REMARK 465 PRO A 17
REMARK 465 PRO A 18
REMARK 465 PRO A 19
REMARK 465 ALA A 20
REMARK 465 ARG A 21
REMARK 465 ARG A 22
REMARK 465 CYS A 23
REMARK 465 LEU A 24
REMARK 465 PRO A 25
REMARK 465 LEU A 458
REMARK 465 GLN A 459
REMARK 465 TYR A 460
REMARK 465 SER A 461
REMARK 465 HIS A 462
REMARK 465 PHE A 463
REMARK 465 SER A 464
REMARK 465 ASP A 465
REMARK 465 ALA A 466
REMARK 465 SER A 467
REMARK 465 SER A 468
REMARK 465 SER A 469
REMARK 465 PRO A 470
REMARK 465 ALA A 471
REMARK 465 ASP A 472
REMARK 465 GLY A 473
REMARK 465 GLY A 474
REMARK 465 GLU A 475
REMARK 465 ASN A 476
REMARK 465 LEU A 477
REMARK 465 TYR A 478
REMARK 465 PHE A 479
REMARK 465 GLN A 480
REMARK 465 GLY B -2
REMARK 465 PRO B -1
REMARK 465 SER B 0
REMARK 465 GLN B 1
REMARK 465 SER B 119
REMARK 465 ALA B 120
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O LYS A 249 OG1 THR A 252 2.11
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 SER A 28 -173.81 -175.65
REMARK 500 ASN A 65 37.51 -98.41
REMARK 500 ASP A 164 -163.24 -79.04
REMARK 500 TYR A 216 -13.34 77.53
REMARK 500 ILE A 217 -60.77 -125.36
REMARK 500 CYS A 237 18.55 -140.83
REMARK 500 LEU A 253 -9.30 78.53
REMARK 500 LYS A 261 45.56 -86.74
REMARK 500 LEU A 262 -35.07 -131.51
REMARK 500 LEU A 301 50.58 -93.60
REMARK 500 MET A 377 37.52 -94.76
REMARK 500 SER B 25 -179.95 -170.03
REMARK 500 PHE B 29 -10.25 70.69
REMARK 500 TRP B 47 128.14 -35.30
REMARK 500 ASP B 57 73.67 -100.51
REMARK 500 ALA B 92 -174.65 -171.94
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: EMD-12141 RELATED DB: EMDB
REMARK 900 CRYO-EM STRUCTURE OF THE PROTON COUPLED FOLATE TRANSPORTER AT PH
REMARK 900 6.0 BOUND TO PEMETREXED
DBREF 7BC7 A 1 473 UNP E6Y8U5 E6Y8U5_CHICK 1 473
DBREF 7BC7 B -2 120 PDB 7BC7 7BC7 -2 120
SEQADV 7BC7 GLY A 474 UNP E6Y8U5 EXPRESSION TAG
SEQADV 7BC7 GLU A 475 UNP E6Y8U5 EXPRESSION TAG
SEQADV 7BC7 ASN A 476 UNP E6Y8U5 EXPRESSION TAG
SEQADV 7BC7 LEU A 477 UNP E6Y8U5 EXPRESSION TAG
SEQADV 7BC7 TYR A 478 UNP E6Y8U5 EXPRESSION TAG
SEQADV 7BC7 PHE A 479 UNP E6Y8U5 EXPRESSION TAG
SEQADV 7BC7 GLN A 480 UNP E6Y8U5 EXPRESSION TAG
SEQRES 1 A 480 MET ALA ALA PRO SER ASP PRO PRO THR ALA ALA THR PRO
SEQRES 2 A 480 PRO ALA PRO PRO PRO PRO ALA ARG ARG CYS LEU PRO ALA
SEQRES 3 A 480 PRO SER VAL GLU PRO LEU LEU PHE LEU ALA THR LEU ALA
SEQRES 4 A 480 LEU GLY LEU GLN VAL PRO LEU ALA THR GLN TYR LEU TRP
SEQRES 5 A 480 ASP ARG LEU GLY ALA GLU ARG GLY TYR VAL GLY PRO ASN
SEQRES 6 A 480 ALA SER SER PRO HIS GLY CYS GLY ASN GLY SER GLY ALA
SEQRES 7 A 480 VAL ASP PRO LEU ARG GLU GLU VAL GLU ALA LEU VAL ALA
SEQRES 8 A 480 HIS TRP ASN LEU CYS ILE ASN LEU GLY GLY PHE PHE VAL
SEQRES 9 A 480 GLY LEU PHE SER VAL THR LEU PHE GLY PRO TRP SER ASP
SEQRES 10 A 480 SER VAL GLY ARG ARG PRO VAL LEU VAL LEU PRO ALA VAL
SEQRES 11 A 480 GLY MET ALA VAL GLN ALA ALA VAL TYR LEU LEU VAL MET
SEQRES 12 A 480 TYR LEU ARG LEU HIS VAL ALA TYR LEU LEU LEU GLY ARG
SEQRES 13 A 480 ILE ILE SER GLY LEU LEU GLY ASP TYR ASN LEU ILE LEU
SEQRES 14 A 480 ALA GLY CYS PHE ALA SER VAL ALA ASP SER SER ASN GLN
SEQRES 15 A 480 ARG THR ARG THR PHE ARG VAL ALA ILE LEU GLU ALA CYS
SEQRES 16 A 480 LEU GLY VAL ALA GLY MET VAL ALA SER VAL GLY GLY GLY
SEQRES 17 A 480 GLN TRP ARG LYS ALA GLU GLY TYR ILE ASN PRO PHE TRP
SEQRES 18 A 480 LEU VAL LEU ALA ALA SER LEU ALA ALA ALA LEU TYR ALA
SEQRES 19 A 480 ALA LEU CYS LEU GLN GLU THR VAL LYS GLN ARG ARG ALA
SEQRES 20 A 480 ALA LYS LEU LEU THR LEU GLN HIS TYR LYS ALA VAL TYR
SEQRES 21 A 480 LYS LEU TYR THR ALA PRO GLU ASP LEU SER SER ARG ARG
SEQRES 22 A 480 LYS LEU ALA LEU TYR SER LEU ALA PHE PHE LEU LEU VAL
SEQRES 23 A 480 THR VAL HIS PHE GLY THR LYS ASP LEU TYR VAL LEU TYR
SEQRES 24 A 480 GLU LEU GLY SER PRO LEU CYS TRP ALA SER ASP LEU ILE
SEQRES 25 A 480 GLY TYR GLY SER ALA ALA SER TYR LEU ALA TYR LEU SER
SEQRES 26 A 480 SER LEU GLY GLY LEU ARG LEU LEU GLN LEU CYS LEU GLU
SEQRES 27 A 480 ASP THR TRP VAL ALA GLU ILE GLY LEU ILE SER ASN ILE
SEQRES 28 A 480 ALA GLY LEU VAL VAL ILE SER LEU ALA THR THR THR PRO
SEQRES 29 A 480 LEU MET PHE THR GLY TYR GLY ILE MET PHE LEU SER MET
SEQRES 30 A 480 ALA ALA THR PRO VAL ILE ARG ALA LYS LEU SER LYS LEU
SEQRES 31 A 480 VAL SER GLU THR GLU GLN GLY ALA LEU PHE ALA SER VAL
SEQRES 32 A 480 ALA CYS VAL GLU GLY LEU CYS SER LEU VAL ALA THR GLY
SEQRES 33 A 480 VAL PHE ASN SER LEU TYR PRO SER THR LEU HIS PHE MET
SEQRES 34 A 480 ARG GLY PHE PRO PHE LEU PHE GLY ALA ILE LEU LEU LEU
SEQRES 35 A 480 ILE PRO ALA ALA ILE MET GLY TRP ILE GLU ILE GLN ASP
SEQRES 36 A 480 SER ASN LEU GLN TYR SER HIS PHE SER ASP ALA SER SER
SEQRES 37 A 480 SER PRO ALA ASP GLY GLY GLU ASN LEU TYR PHE GLN
SEQRES 1 B 123 GLY PRO SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY
SEQRES 2 B 123 LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA
SEQRES 3 B 123 ALA SER GLY PHE THR PHE SER ARG TYR TRP MET TYR TRP
SEQRES 4 B 123 VAL ARG GLN ALA PRO GLY LYS GLY PRO GLU TRP LEU SER
SEQRES 5 B 123 HIS MET ASN PRO SER GLY SER ASP ILE LYS TYR THR ASP
SEQRES 6 B 123 SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA
SEQRES 7 B 123 LYS ASN THR LEU TYR LEU GLN MET ASN SER LEU LYS PRO
SEQRES 8 B 123 ASP ASP THR ALA VAL TYR TYR CYS VAL ALA ASP ARG ARG
SEQRES 9 B 123 ALA LEU GLY SER PRO GLU TYR TRP GLY GLN GLY THR GLN
SEQRES 10 B 123 VAL THR VAL SER SER ALA
HET LYA A 501 31
HETNAM LYA 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-
HETNAM 2 LYA D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC
HETNAM 3 LYA ACID
HETSYN LYA LY231514
FORMUL 3 LYA C20 H21 N5 O6
HELIX 1 AA1 VAL A 29 ARG A 59 1 31
HELIX 2 AA2 ASP A 80 GLY A 120 1 41
HELIX 3 AA3 GLY A 120 ARG A 146 1 27
HELIX 4 AA4 ALA A 150 LEU A 162 1 13
HELIX 5 AA5 ASP A 164 ASP A 178 1 15
HELIX 6 AA6 THR A 184 ARG A 211 1 28
HELIX 7 AA7 ASN A 218 CYS A 237 1 20
HELIX 8 AA8 TYR A 256 THR A 264 1 9
HELIX 9 AA9 SER A 270 GLU A 300 1 31
HELIX 10 AB1 ALA A 308 GLN A 334 1 27
HELIX 11 AB2 GLU A 338 LEU A 359 1 22
HELIX 12 AB3 THR A 362 MET A 373 1 12
HELIX 13 AB4 LEU A 375 MET A 377 5 3
HELIX 14 AB5 ALA A 378 VAL A 391 1 14
HELIX 15 AB6 GLU A 395 THR A 425 1 31
HELIX 16 AB7 GLY A 431 LEU A 441 1 11
HELIX 17 AB8 LEU A 441 SER A 456 1 16
HELIX 18 AB9 LYS B 87 THR B 91 5 5
SHEET 1 AA1 4 GLN B 3 GLU B 6 0
SHEET 2 AA1 4 LEU B 18 SER B 25 -1 O ALA B 23 N VAL B 5
SHEET 3 AA1 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18
SHEET 4 AA1 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80
SHEET 1 AA2 3 SER B 49 MET B 51 0
SHEET 2 AA2 3 TRP B 33 ARG B 38 -1 N MET B 34 O MET B 51
SHEET 3 AA2 3 ALA B 98 ASP B 99 -1 O ASP B 99 N TRP B 33
SHEET 1 AA3 4 SER B 49 MET B 51 0
SHEET 2 AA3 4 TRP B 33 ARG B 38 -1 N MET B 34 O MET B 51
SHEET 3 AA3 4 ALA B 92 TYR B 95 -1 O TYR B 95 N VAL B 37
SHEET 4 AA3 4 THR B 113 VAL B 115 -1 O VAL B 115 N ALA B 92
SSBOND 1 CYS A 72 CYS A 306 1555 1555 2.03
SSBOND 2 CYS B 22 CYS B 96 1555 1555 2.04
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000